Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java

@@ -131,7 +131,7 @@ public class AlignmentContextUtils {
         }
     }
 
-    public static Map<String, AlignmentContext> splitContextBySampleName(ReadBackedPileup pileup, String assumedSingleSample) {
+    public static Map<String, AlignmentContext> splitContextBySampleName(ReadBackedPileup pileup) {
         return splitContextBySampleName(new AlignmentContext(pileup.getLocation(), pileup));
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java

@@ -14,7 +14,8 @@ import java.util.List;
 
 
 /**
- * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele)
+ * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele).
+ * Note that the base quality rank sum test can not be calculated for homozygous sites.
  */
 public class BaseQualityRankSumTest extends RankSumTest {
     public List<String> getKeyNames() { return Arrays.asList("BaseQRankSum"); }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -46,7 +46,8 @@ import java.util.*;
 /**
  * Phred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation
  * being seen on only the forward or only the reverse strand) in the reads? More bias is
- * indicative of false positive calls.
+ * indicative of false positive calls.  Note that the fisher strand test may not be
+ * calculated for certain complex indel cases or for multi-allelic sites.
  */
 public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotation {
     private static final String FS = "FS";

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -52,6 +52,8 @@ import java.util.*;
 /**
  * Consistency of the site with two (and only two) segregating haplotypes. Higher scores
  * are indicative of regions with bad alignments, often leading to artifactual SNP and indel calls.
+ * Note that the Haplotype Score is only calculated for sites with read coverage; also, for SNPs, the
+ * site must be bi-allelic.
  */
 public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnotation {
     private final static boolean DEBUG = false;
@@ -180,12 +182,12 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
             final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
 
             List<Haplotype>hlist = new ArrayList<Haplotype>();
-            hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60));
+            hlist.add(new Haplotype(haplotype1.getBases(), 60));
 
             for (int k=1; k < haplotypesToCompute; k++) {
                 Haplotype haplotype2 = consensusHaplotypeQueue.poll();
                 if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found
-                hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20));
+                hlist.add(new Haplotype(haplotype2.getBases(), 20));
             }
             return hlist;
         } else
@@ -229,8 +231,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
     }
 
     private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, final Haplotype haplotypeB) {
-        final byte[] a = haplotypeA.getBasesAsBytes();
+        final byte[] a = haplotypeA.getBases();
-        final byte[] b = haplotypeB.getBasesAsBytes();
+        final byte[] b = haplotypeB.getBases();
 
         if (a.length != b.length) {
             throw new ReviewedStingException("Haplotypes a and b must be of same length");
@@ -313,7 +315,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         // actually be a miscall in a matching direction, which would happen at a e / 3 rate.  If b != c, then
         // the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch.
         // so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n
-        final byte[] haplotypeBases = haplotype.getBasesAsBytes();
+        final byte[] haplotypeBases = haplotype.getBases();
         final SAMRecord read = p.getRead();
         byte[] readBases = read.getReadBases();
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java

@@ -23,7 +23,8 @@ import java.util.Map;
  *
  * A continuous generalization of the Hardy-Weinberg test for disequilibrium that works
  * well with limited coverage per sample.  See the 1000 Genomes Phase I release for
- * more information.
+ * more information.  Note that the Inbreeding Coefficient will not be calculated for files
+ * with fewer than a minimum (generally 10) number of samples.
  */
 public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnnotation {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java

@@ -16,6 +16,7 @@ import java.util.List;
 
 /**
  * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele)
+ * Note that the mapping quality rank sum test can not be calculated for homozygous sites.
  */
 public class MappingQualityRankSumTest extends RankSumTest {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java

@@ -19,7 +19,8 @@ import java.util.Map;
 /**
  * Variant confidence (given as (AB+BB)/AA from the PLs) / unfiltered depth.
  *
- * Low scores are indicative of false positive calls and artifacts.
+ * Low scores are indicative of false positive calls and artifacts.  Note that QualByDepth requires sequencing
+ * reads associated with the samples with polymorphic genotypes.
  */
 public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java

@@ -20,6 +20,7 @@ import java.util.List;
 
 /**
  * The phred-scaled p-value (u-based z-approximation) from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error).
+ * Note that the read position rank sum test can not be calculated for homozygous sites.
  */
 public class ReadPosRankSumTest extends RankSumTest {
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -164,10 +164,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
     @Argument(fullName="list", shortName="ls", doc="List the available annotations and exit")
     protected Boolean LIST = false;
 
-    @Hidden
-    @Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
-    protected String ASSUME_SINGLE_SAMPLE = null;
-
     @Hidden
     @Argument(fullName="vcfContainsOnlyIndels", shortName="dels",doc="Use if you are annotating an indel vcf, currently VERY experimental", required = false)
     protected boolean indelsOnly = false;
@@ -213,11 +209,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         List<String> rodName = Arrays.asList(variantCollection.variants.getName());
         Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
 
-        // if there are no valid samples, warn the user
-        if ( samples.size() == 0 ) {
-            logger.warn("There are no samples input at all; use the --sampleName argument to specify one if desired.");
-        }
-
         if ( USE_ALL_ANNOTATIONS )
             engine = new VariantAnnotatorEngine(annotationsToExclude, this, getToolkit());
         else
@@ -301,9 +292,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         Map<String, AlignmentContext> stratifiedContexts;
         if ( BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1 ) {
             if ( ! context.hasExtendedEventPileup() ) {
-                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup(), ASSUME_SINGLE_SAMPLE);
+                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getBasePileup());
             } else {
-                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup(), ASSUME_SINGLE_SAMPLE);
+                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(context.getExtendedEventPileup());
             }
             if ( stratifiedContexts != null ) {
                 annotatedVCs = new ArrayList<VariantContext>(VCs.size());

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java

@@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.util.HashSet;
 import java.util.Set;
-import java.util.TreeSet;
 
 
 /**
@@ -71,12 +70,7 @@ public class UGCalcLikelihoods extends LocusWalker<VariantCallContext, Integer>
 
     public void initialize() {
         // get all of the unique sample names
-        // if we're supposed to assume a single sample, do so
+        Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
-        Set<String> samples = new TreeSet<String>();
-        if ( UAC.ASSUME_SINGLE_SAMPLE != null )
-            samples.add(UAC.ASSUME_SINGLE_SAMPLE);
-        else
-            samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
 
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -96,11 +96,6 @@ public class UnifiedArgumentCollection {
     @Input(fullName="alleles", shortName = "alleles", doc="The set of alleles at which to genotype when in GENOTYPE_MODE = GENOTYPE_GIVEN_ALLELES", required=false)
     public RodBinding<VariantContext> alleles;
 
-    // control the error modes
-    @Hidden
-    @Argument(fullName = "assume_single_sample_reads", shortName = "single_sample", doc = "The single sample that we should assume is represented in the input bam (and therefore associate with all reads regardless of whether they have read groups)", required = false)
-    public String ASSUME_SINGLE_SAMPLE = null;
-
     /**
      * The minimum confidence needed in a given base for it to be used in variant calling.  Note that the base quality of a base
      * is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value.
@@ -170,7 +165,6 @@ public class UnifiedArgumentCollection {
         uac.GenotypingMode = GenotypingMode;
         uac.OutputMode = OutputMode;
         uac.COMPUTE_SLOD = COMPUTE_SLOD;
-        uac.ASSUME_SINGLE_SAMPLE = ASSUME_SINGLE_SAMPLE;
         uac.STANDARD_CONFIDENCE_FOR_CALLING = STANDARD_CONFIDENCE_FOR_CALLING;
         uac.STANDARD_CONFIDENCE_FOR_EMITTING = STANDARD_CONFIDENCE_FOR_EMITTING;
         uac.MIN_BASE_QUALTY_SCORE = MIN_BASE_QUALTY_SCORE;

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -206,12 +206,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
      **/
     public void initialize() {
         // get all of the unique sample names
-        // if we're supposed to assume a single sample, do so
+        Set<String> samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
-        Set<String> samples = new TreeSet<String>();
-        if ( UAC.ASSUME_SINGLE_SAMPLE != null )
-            samples.add(UAC.ASSUME_SINGLE_SAMPLE);
-        else
-            samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
 
         // initialize the verbose writer
         if ( verboseWriter != null )

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -106,12 +106,7 @@ public class UnifiedGenotyperEngine {
     // ---------------------------------------------------------------------------------------------------------
     @Requires({"toolkit != null", "UAC != null"})
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null,
+        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
-                // get the number of samples
-                // if we're supposed to assume a single sample, do so
-                UAC.ASSUME_SINGLE_SAMPLE != null ?
-                        new TreeSet<String>(Arrays.asList(UAC.ASSUME_SINGLE_SAMPLE)) :
-                        SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
     }
 
     @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0"})
@@ -253,7 +248,7 @@ public class UnifiedGenotyperEngine {
                 pileup = rawContext.getExtendedEventPileup();
             else if (rawContext.hasBasePileup())
                 pileup = rawContext.getBasePileup();
-            stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
+            stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
 
             vc = annotationEngine.annotateContext(tracker, ref, stratifiedContexts, vc);
         }
@@ -435,7 +430,7 @@ public class UnifiedGenotyperEngine {
                 pileup = rawContext.getExtendedEventPileup();
             else if (rawContext.hasBasePileup())
                 pileup = rawContext.getBasePileup();
-            stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
+            stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
 
             vcCall = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, vcCall);
         }
@@ -569,7 +564,7 @@ public class UnifiedGenotyperEngine {
                     return null;
 
                 // stratify the AlignmentContext and cut by sample
-                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
+                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
 
             } else {
 
@@ -586,12 +581,12 @@ public class UnifiedGenotyperEngine {
                     return null;
 
                 // stratify the AlignmentContext and cut by sample
-                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup, UAC.ASSUME_SINGLE_SAMPLE);
+                stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
             }
         } else if ( model == GenotypeLikelihoodsCalculationModel.Model.SNP ) {
 
             // stratify the AlignmentContext and cut by sample
-            stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup(), UAC.ASSUME_SINGLE_SAMPLE);
+            stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup());
 
             if( !(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) ) {
                 int numDeletions = 0;

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java

@@ -205,7 +205,7 @@ public class HaplotypeIndelErrorModel {
 
                 byte haplotypeBase;
                 if (haplotypeIndex < RIGHT_ALIGN_INDEX)
-                    haplotypeBase = haplotype.getBasesAsBytes()[haplotypeIndex];
+                    haplotypeBase = haplotype.getBases()[haplotypeIndex];
                 else
                     haplotypeBase = (byte)0; // dummy
 
@@ -217,7 +217,7 @@ public class HaplotypeIndelErrorModel {
                 if (readQual > 3)
                     pRead += pBaseRead;
                 haplotypeIndex++;
-                if (haplotypeIndex >= haplotype.getBasesAsBytes().length)
+                if (haplotypeIndex >= haplotype.getBases().length)
                     haplotypeIndex = RIGHT_ALIGN_INDEX;
                 //System.out.format("H:%c R:%c RQ:%d HI:%d %4.5f %4.5f\n", haplotypeBase, readBase, (int)readQual, haplotypeIndex, pBaseRead, pRead);
              }
@@ -227,8 +227,8 @@ public class HaplotypeIndelErrorModel {
                 System.out.println(read.getReadName());
                 System.out.print("Haplotype:");
 
-                for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
+                for (int k=0; k <haplotype.getBases().length; k++) {
-                    System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+                    System.out.format("%c ", haplotype.getBases()[k]);
                 }
                 System.out.println();
 
@@ -246,8 +246,8 @@ public class HaplotypeIndelErrorModel {
 
                 System.out.println("Haplotype:");
 
-                for (int k=initialIndexInHaplotype; k <haplotype.getBasesAsBytes().length; k++) {
+                for (int k=initialIndexInHaplotype; k <haplotype.getBases().length; k++) {
-                    System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+                    System.out.format("%c ", haplotype.getBases()[k]);
                 }
                 System.out.println();
 
@@ -275,7 +275,7 @@ public class HaplotypeIndelErrorModel {
 
                 byte haplotypeBase;
                 if (indX > LEFT_ALIGN_INDEX && indX < RIGHT_ALIGN_INDEX)
-                    haplotypeBase = haplotype.getBasesAsBytes()[indX-1];
+                    haplotypeBase = haplotype.getBases()[indX-1];
                 else
                     haplotypeBase = readBase;
 
@@ -296,8 +296,8 @@ public class HaplotypeIndelErrorModel {
             System.out.println(read.getReadName());
             System.out.print("Haplotype:");
 
-            for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
+            for (int k=0; k <haplotype.getBases().length; k++) {
-                System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
+                System.out.format("%c ", haplotype.getBases()[k]);
             }
             System.out.println();
 

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -817,7 +817,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         // For now, we will just arbitrarily add 10 to the mapping quality. [EB, 6/7/2010].
                         // TODO -- we need a better solution here
                         GATKSAMRecord read = aRead.getRead();
-                        read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
+                        if ( read.getMappingQuality() != 255 ) // 255 == Unknown, so don't modify it
+                            read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
 
                         // before we fix the attribute tags we first need to make sure we have enough of the reference sequence
                         int neededBasesToLeft = leftmostIndex - read.getAlignmentStart();

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java

@@ -381,7 +381,7 @@ public class PairHMMIndelErrorModel {
         // todo -- refactor into separate function
         for (Allele a: haplotypeMap.keySet()) {
             Haplotype haplotype = haplotypeMap.get(a);
-            byte[] haplotypeBases = haplotype.getBasesAsBytes();
+            byte[] haplotypeBases = haplotype.getBases();
             double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length];
             double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length];
 
@@ -555,7 +555,7 @@ public class PairHMMIndelErrorModel {
                         long indStart = start - haplotype.getStartPosition();
                         long indStop =  stop - haplotype.getStartPosition();
 
-                        byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(),
+                        byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
                                 (int)indStart, (int)indStop);
 
                         double readLikelihood;

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypes.java

@@ -1,118 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.phasing;
-
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-
-import java.util.*;
-
-/**
- * Merges read-back-phased and phase-by-transmission files.
- */
-public class MergeAndMatchHaplotypes extends RodWalker<Integer, Integer> {
-    @Output
-    protected VCFWriter vcfWriter = null;
-
-    @Input(fullName="pbt", shortName = "pbt", doc="Input VCF truth file", required=true)
-    public RodBinding<VariantContext> pbtTrack;
-
-    @Input(fullName="rbp", shortName = "rbp", doc="Input VCF truth file", required=true)
-    public RodBinding<VariantContext> rbpTrack;
-
-    private Map<String, Genotype> pbtCache = new HashMap<String, Genotype>();
-    private Map<String, Genotype> rbpCache = new HashMap<String, Genotype>();
-
-    private final String SOURCE_NAME = "MergeReadBackedAndTransmissionPhasedVariants";
-
-    public void initialize() {
-        ArrayList<String> rodNames = new ArrayList<String>();
-        rodNames.add(pbtTrack.getName());
-
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
-        Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
-        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
-        headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit()));
-
-        vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples));
-    }
-
-    @Override
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        if (tracker != null) {
-            Collection<VariantContext> pbts = tracker.getValues(pbtTrack, ref.getLocus());
-            Collection<VariantContext> rbps = tracker.getValues(rbpTrack, ref.getLocus());
-
-            VariantContext pbt = pbts.iterator().hasNext() ? pbts.iterator().next() : null;
-            VariantContext rbp = rbps.iterator().hasNext() ? rbps.iterator().next() : null;
-
-            if (pbt != null && rbp != null) {
-                Map<String, Genotype> genotypes = pbt.getGenotypes();
-
-                if (!rbp.isFiltered()) {
-                    for (String sample : rbp.getSampleNames()) {
-                        Genotype rbpg = rbp.getGenotype(sample);
-                        Genotype pbtg = pbt.getGenotype(sample);
-
-                        // Propagate read-backed phasing information to genotypes unphased by transmission
-                        //if (!pbtg.isPhased() && rbpCache.containsKey(sample)) {
-                        if (!pbtg.isPhased() && rbpg.isPhased() && rbpCache.containsKey(sample)) {
-                            boolean orientationMatches = rbpCache.get(sample).sameGenotype(pbtCache.get(sample), false);
-
-                            if (orientationMatches) {
-                                pbtg = rbpg;
-                            } else {
-                                List<Allele> fwdAlleles = rbpg.getAlleles();
-                                List<Allele> revAlleles = new ArrayList<Allele>();
-
-                                for (int i = fwdAlleles.size() - 1; i >= 0; i--) {
-                                    revAlleles.add(fwdAlleles.get(i));
-                                }
-
-                                pbtg = new Genotype(sample, revAlleles, rbpg.getNegLog10PError(), rbpg.getFilters(), rbpg.getAttributes(), rbpg.isPhased());
-                            }
-                        }
-
-                        genotypes.put(sample, pbtg);
-
-                        // Update the cache
-                        if (/*rbpg.isPhased() &&*/ rbpg.isHet()) {
-                            rbpCache.put(sample, rbpg);
-                            pbtCache.put(sample, pbtg);
-                        } else if (!rbpg.isPhased()) {
-                            rbpCache.remove(sample);
-                            pbtCache.remove(sample);
-                        }
-                    }
-                }
-
-                VariantContext newvc = new VariantContext(SOURCE_NAME, pbt.getChr(), pbt.getStart(), pbt.getStart(), pbt.getAlleles(), genotypes, pbt.getNegLog10PError(), pbt.getFilters(), pbt.getAttributes());
-                vcfWriter.add(newvc);
-            }
-        }
-
-        return null;
-    }
-
-    @Override
-    public Integer reduceInit() {
-        return null;
-    }
-
-    @Override
-    public Integer reduce(Integer value, Integer sum) {
-        return null;
-    }
-}

public/java/src/org/broadinstitute/sting/utils/Haplotype.java

@@ -33,8 +33,8 @@ import java.util.LinkedHashMap;
 import java.util.List;
 
 public class Haplotype {
-    protected byte[] bases = null;
+    protected final byte[] bases;
-    protected double[] quals = null;
+    protected final double[] quals;
     private GenomeLoc genomeLocation = null;
     private boolean isReference = false;
  
@@ -69,6 +69,11 @@ public class Haplotype {
         this.isReference = isRef;
     }
 
+    @Override
+    public boolean equals( Object h ) {
+        return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases);
+    }
+
     public double getQualitySum() {
         double s = 0;
         for (int k=0; k < bases.length; k++) {
@@ -88,7 +93,7 @@ public class Haplotype {
     public double[] getQuals() {
         return quals;
     }
-    public byte[] getBasesAsBytes() {
+    public byte[] getBases() {
         return bases;
     }
 
@@ -100,7 +105,6 @@ public class Haplotype {
         return genomeLocation.getStop();
     }
 
-
     public boolean isReference() {
         return isReference;
     }

public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java

@@ -1,10 +1,5 @@
 package org.broadinstitute.sting.utils;
 
-import com.google.java.contract.Ensures;
-import com.google.java.contract.Invariant;
-import com.google.java.contract.Requires;
-
-import java.io.PrintStream;
 
 /**
  * A useful simple system for timing code.  This code is not thread safe!
@@ -13,11 +8,6 @@ import java.io.PrintStream;
  * Date: Dec 10, 2010
  * Time: 9:07:44 AM
  */
-@Invariant({
-        "elapsed >= 0",
-        "startTime >= 0",
-        "name != null",
-        "! running || startTime > 0"})
 public class SimpleTimer {
     final private String name;
     private long elapsed = 0l;
@@ -27,7 +17,6 @@ public class SimpleTimer {
     /**
      * Creates an anonymous simple timer
      */
-    @Ensures("name != null && name.equals(\"Anonymous\")")
     public SimpleTimer() {
         this("Anonymous");
     }
@@ -36,8 +25,6 @@ public class SimpleTimer {
      * Creates a simple timer named name
      * @param name of the timer, must not be null
      */
-    @Requires("name != null")
-    @Ensures("this.name != null && this.name.equals(name)")
     public SimpleTimer(String name) {
         this.name = name;
     }
@@ -45,7 +32,6 @@ public class SimpleTimer {
     /**
      * @return the name associated with this timer
      */
-    @Ensures("result != null")
     public synchronized String getName() {
         return name;
     }
@@ -56,8 +42,6 @@ public class SimpleTimer {
      *
      * @return this object, for programming convenience
      */
-    @Requires("running == false")
-    @Ensures({"result != null", "elapsed == 0l"})
     public synchronized SimpleTimer start() {
         elapsed = 0l;
         restart();
@@ -71,8 +55,6 @@ public class SimpleTimer {
      *
      * @return this object, for programming convenience
      */
-    @Requires("running == false")
-    @Ensures("result != null")
     public synchronized SimpleTimer restart() {
         running = true;
         startTime = currentTime();
@@ -99,8 +81,6 @@ public class SimpleTimer {
      *
      * @return this object, for programming convenience
      */
-    @Requires("running == true")
-    @Ensures({"result != null", "elapsed >= old(elapsed)", "running == false"})
     public synchronized SimpleTimer stop() {
         running = false;
         elapsed += currentTime() - startTime;
@@ -113,9 +93,6 @@ public class SimpleTimer {
      *
      * @return this time, in seconds
      */
-    @Ensures({
-            "result >= (elapsed/1000.0)",
-            "result >= 0"})
     public synchronized double getElapsedTime() {
         return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0;
     }

public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -124,6 +124,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("using expression", spec);
     }
 
+    @Test
+    public void testUsingExpressionWithID() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " --resource:foo " + validationDataLocation + "targetAnnotations.vcf -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.ID -L " + validationDataLocation + "vcfexample3empty.vcf", 1,
+                Arrays.asList("4a6f0675242f685e9072c1da5ad9e715"));
+        executeTest("using expression with ID", spec);
+    }
+
     @Test
     public void testTabixAnnotations() {
         final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";

public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java

@@ -1,28 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.phasing;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
-
-import java.util.Arrays;
-
-public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest {
-    private static String mergeAndMatchHaplotypesTestDataRoot = validationDataLocation + "/MergeAndMatchHaplotypes";
-    private static String fundamentalTestPBTVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.vcf";
-    private static String fundamentalTestRBPVCF = mergeAndMatchHaplotypesTestDataRoot + "/" + "FundamentalsTest.pbt.rbp.vcf";
-
-    @Test
-    public void testBasicFunctionality() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                buildCommandLine(
-                        "-T MergeAndMatchHaplotypes",
-                        "-R " + b37KGReference,
-                        "--pbt " + fundamentalTestPBTVCF,
-                        "--rbp " + fundamentalTestRBPVCF,
-                        "-o %s"
-                ),
-                1,
-                Arrays.asList("")
-        );
-        executeTest("testBasicMergeAndMatchHaplotypesFunctionality", spec);
-    }
-}

public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -9,7 +9,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     private static String variantEvalTestDataRoot = validationDataLocation + "VariantEval";
     private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf";
     private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf";
-    private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf";
+    private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.NA12045.vcf";
 
     private static String cmdRoot = "-T VariantEval" +
             " -R " + b36KGReference;
@@ -359,7 +359,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
 
     @Test
     public void testPerSampleAndSubsettedSampleHaveSameResults() {
-        String md5 = "b0565ac61b2860248e4abd478a177b5e";
+        String md5 = "7425ca5c439afd7bb33ed5cfea02c2b3";
 
         WalkerTestSpec spec = new WalkerTestSpec(
                 buildCommandLine(
@@ -369,7 +369,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "--eval " + fundamentalTestSNPsVCF,
                         "-noEV",
                         "-EV CompOverlap",
-                        "-sn HG00625",
+                        "-sn NA12045",
                         "-noST",
                         "-L " + fundamentalTestSNPsVCF,
                         "-o %s"